I've seen mentioned that annotations and highlights in PDFs get exported in a separate file. Now I am sure plenty of you guys do use Kindles to read journal articles or have a comparable need to annotate PDFs. How easy is it for you to annotate the files and use the annotations on your home computer/PDF reader(which one?)? How easy is it for you to implement those annotations into referencing software (ie, endnote?)

Asking because I find most comparable questions are 2 years old. Firmware changes, and sometimes gets better (or so they say?)

Asking with the Kindle Touch in mind.
Cheers,

Pismire

PS: bonus questions: what is your favorite citation software? Endnote does not let you easily grab your PDFs from the library, simply uses the PDF name for the folder name, and just in general seems to have taken 5% of the thought that has been put into Calibre....